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As of Chromium 16, there are currently build issues with NaCl on Ubuntu. I believe this has something to do with compiling Chromium with the Debian security hardening wrapper. A bunch of launchpad bugs have been filed semi-related to this, but I think LP#882942 is the main one triaged to NaCl on Chromium.

Unfortunately this means if you want to use NaCl in Ubuntu, you must install the official Google Chrome build.